a. I modified a few little things in that story and made it a much better story than you wrote it.
(You wrote that story. I made it better by modifying a few little things.)
b. I added a few things to that machine and now it is a better machine than you made it.
(You made that machine. I made it better.)

a) I modified a few little things in the story and made it a much better story than that which you'd written.
b. I added a few things to the machine and now it is a better machine than that which you'd made.

If I were to use the last three words of your sentences, BonnieL, I'd hyphenate them to "what-you-wrote" and "what-you-made", creating singularities of them, in my mind, at least. Heck, I might even hyphenate the last four in my sentences!
The prescriptivist in me will not be cast-out.

a. I modified a few little things in that story and made it a much better story than you wrote it.
(You wrote that story. I made it better by modifying a few little things.)
b. I added a few things to that machine and now it is a better machine than you made it.
(You made that machine. I made it better.)

I agree with Bonnie that the "it" on the end of the sentence looks ugly but without "it" we're not really clear who wrote the original story.

"I modified a few little things in that story and made it a much better story than what you wrote."

Consider that Joe and Bob both wrote stories. I tweaked Bob's story and created a story that was better than the one that Joe wrote. I'd just take the most direct route

"I modified a few things in the story that you wrote and made it much better."

PS Azz, did you and Navi and Digitalen all go to the same school, or grow up in the same family or, perhaps, just share the same body?

Actually Navi and I are married. We work together and sometimes have arguments about grammar (not a big deal). Phil has been informed of this. It is no big secret.But you will make a good detective. I thought my questions were a lot better than his!

I don't have any idea who Digitalen is. If Navi is up to some mischief, he has kept me in the dark!
(I am joking. It is not him.)

Ahh, yes. I wasn't so sure that Digitalen was was in the mix, although there are similarities in the types of questions and the way in which they are presented. I would have bet that Navi and Azz were different screen names for the same person...not that it matters, at all.
Thanks